Estimating microhaplotype allele frequencies from low-coverage or pooled sequencing data

High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing

(2022) Michael Schneider et al.   Plant Methods

Single‐parentage assignments reveal negative‐assortative mating in an endangered salmonid

(2022) Craig A. Steele et al.   Ecology and Evolution

Sex locus and sex markers identification using whole genome pool-sequencing approach in the largemouth bass (Micropterus Salmoides L.)

(2022) Ming Wen et al.   AQUACULTURE

Population structure in a continuously distributed coastal marine species, the harbor porpoise, based on microhaplotypes derived from poor‐quality samples

(2021) Phillip A. Morin et al.   MOLECULAR ECOLOGY

Benchmarking the performance of Pool‐seq SNP callers using simulated and real sequencing data

(2021) Sara Guirao‐Rico et al.   Molecular Ecology Resources

HTSlib: C library for reading/writing high-throughput sequencing data

(2021) James K Bonfield et al.   GigaScience

A chromosome-level genome assembly for the Pacific oyster Crassostrea gigas

(2021) Carolina Peñaloza et al.   GigaScience

A beginner's guide to low‐coverage whole genome sequencing for population genomics

(2021) Runyang Nicolas Lou et al.   MOLECULAR ECOLOGY

Current status and potential of genomic selection to improve selective breeding in the main aquaculture species of International Council for the Exploration of the Sea (ICES) member countries

(2021) Pierre Boudry et al.   Aquaculture Reports

Grandparent Inference from Genetic Data: The Potential for Parentage‐Based Tagging Programs to Identify Offspring of Hatchery Strays

(2021) Thomas A. Delomas et al.   NORTH AMERICAN JOURNAL OF FISHERIES MANAGEMENT

A New Single Nucleotide Polymorphism Database for North American Atlantic Salmon Generated Through Whole Genome Resequencing

(2020) Guangtu Gao et al.   Frontiers in Genetics

Harnessing genomics to fast-track genetic improvement in aquaculture

(2020) Ross D. Houston et al.   NATURE REVIEWS GENETICS

Genetic stock structure of New Zealand fish and the use of genomics in fisheries management: an overview and outlook

(2020) Yvan Papa et al.   NEW ZEALAND JOURNAL OF ZOOLOGY

Genomic islands of divergence infer a phenotypic landscape in Pacific lamprey

(2020) Jon E. Hess et al.   MOLECULAR ECOLOGY

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

Contemporary genetic structure affects genetic stock identification of steelhead trout in the Snake River basin

(2020) John H. Powell et al.   Ecology and Evolution

Parentage-based tagging improves escapement estimates for ESA-listed adult Chinook salmon and steelhead in the Snake River basin

(2020) John S. Hargrove et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Genomic Selection in Aquaculture: Application, Limitations and Opportunities With Special Reference to Marine Shrimp and Pearl Oysters

(2019) Kyall R. Zenger et al.   Frontiers in Genetics

The future is now: amplicon sequencing and sequence capture usher in the conservation genomics era

(2019) Mariah H. Meek et al.   Molecular Ecology Resources

Parentage‐Based Tagging: Reviewing the Implementation of a New Tool for an Old Problem

(2019) Craig A. Steele et al.   FISHERIES

Dense SNP panels resolve closely related Chinook salmon populations

(2019) Garrett J. McKinney et al.   CANADIAN JOURNAL OF FISHERIES AND AQUATIC SCIENCES

Accurate Allele Frequencies from Ultra-low Coverage Pool-Seq Samples in Evolve-and-Resequence Experiments

(2019) Susanne Tilk et al.   G3-Genes Genomes Genetics

Building a custom large-scale panel of novel microhaplotypes for forensic identification using MiSeq and Ion S5 massively parallel sequencing systems

(2019) M. de la Puente et al.   Forensic Science International-Genetics

Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon

(2019) Smaragda Tsairidou et al.   G3-Genes Genomes Genetics

Evaluation of the Microhaplotypes panel for DNA mixture analyses

(2018) Peng Chen et al.   Forensic Science International-Genetics

Utility of pooled sequencing for association mapping in nonmodel organisms

(2018) Steven J. Micheletti et al.   Molecular Ecology Resources

Genomic Tools and Selective Breeding in Molluscs

(2018) Christopher M. Hollenbeck et al.   Frontiers in Genetics

Selection at a genomic region of major effect is responsible for evolution of complex life histories in anadromous steelhead

(2018) Steven J. Micheletti et al.   BMC EVOLUTIONARY BIOLOGY

Divergence and plasticity shape adaptive potential of the Pacific oyster

(2018) Li Li et al.   Nature Ecology & Evolution

Invited review: A perspective on the future of genomic selection in dairy cattle

(2017) J.I. Weller et al.   JOURNAL OF DAIRY SCIENCE

Whole-genome sequencing approaches for conservation biology: Advantages, limitations and practical recommendations

(2017) Angela P. Fuentes-Pardo et al.   MOLECULAR ECOLOGY

Microhaplotypes provide increased power from short-read DNA sequences for relationship inference

(2017) Diana S. Baetscher et al.   Molecular Ecology Resources

Haplotyping RAD loci: an efficient method to filter paralogs and account for physical linkage

(2017) Stuart C. Willis et al.   Molecular Ecology Resources

Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon

(2017) Hsin-Yuan Tsai et al.   G3-Genes Genomes Genetics

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

(2016) Peter Edge et al.   GENOME RESEARCH

Breaking RAD: an evaluation of the utility of restriction site-associated DNA sequencing for genome scans of adaptation

(2016) David B. Lowry et al.   Molecular Ecology Resources

Genomics in Conservation: Case Studies and Bridging the Gap between Data and Application

(2016) Brittany A. Garner et al.   TRENDS IN ECOLOGY & EVOLUTION

WhatsHap: Weighted Haplotype Assembly for Future-Generation Sequencing Reads

(2015) Murray Patterson et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Evaluation of measures of correctness of genotype imputation in the context of genomic prediction: a review of livestock applications

(2014) M. P. L. Calus et al.   Animal

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

How and why should we implement genomics into conservation?

(2014) Barry J. McMahon et al.   Evolutionary Applications

Current sequencing technology makes microhaplotypes a powerful new type of genetic marker for forensics

(2014) Kenneth K. Kidd et al.   Forensic Science International-Genetics

Population-Genetic Inference from Pooled-Sequencing Data

(2014) Michael Lynch et al.   Genome Biology and Evolution

Personalized Medicine Through SNP Testing for Breast Cancer Risk: Clinical Implementation

(2014) Rebecca Howe et al.   Journal of Genetic Counseling

Genotyping-in-Thousands by sequencing (GT-seq): A cost effective SNP genotyping method based on custom amplicon sequencing

(2014) Nathan R. Campbell et al.   Molecular Ecology Resources

Sequencing pools of individuals — mining genome-wide polymorphism data without big funding

(2014) Christian Schlötterer et al.   NATURE REVIEWS GENETICS

dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms

(2014) Jonathan B. Puritz et al.   PeerJ

A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms

(2013) Quan Chen et al.   BMC GENOMICS

Maximum Likelihood Estimation of Frequencies of Known Haplotypes from Pooled Sequence Data

(2013) D. Kessner et al.   MOLECULAR BIOLOGY AND EVOLUTION

SNP calling by sequencing pooled samples

(2012) Emanuele Raineri et al.   BMC BIOINFORMATICS

Population genomics of Pacific lamprey: adaptive variation in a highly dispersive species

(2012) Jon E. Hess et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Estimation of allele frequency and association mapping using next-generation sequencing data

(2011) Su Kim et al.   BMC BIOINFORMATICS

Improving human forensics through advances in genetics, genomics and molecular biology

(2011) Manfred Kayser et al.   NATURE REVIEWS GENETICS

PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals

(2011) Robert Kofler et al.   PLoS One

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Genotype imputation for genome-wide association studies

(2010) Jonathan Marchini et al.   NATURE REVIEWS GENETICS

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genomic Selection Using Low-Density Marker Panels

(2009) D. Habier et al.   GENETICS